Homecoming
by Diporae
Summary: TMNT 2003, sequel to "Fear", and part 3 of arc. With Raphael finally back to normal, he and Leonardo rush back to the lair to save their brothers from the TCRI robots. However, things aren't always what they seem... Rated for language.
1. Chapter 1

**I still do not own TMNT so please resist suing me.**

**A/N I made some title changes just FYI. I am really bad at deciding on titles so I apologize for the change. Here's a nice short chapter to ease us into Part 3. Enjoy!**

Part 3

Chapter 1

Leonardo was frustrated. I could tell there was nothing he wanted to do more than finish our journey to the lair as fast as possible. Only problem was, he couldn't even stand. Currently, he was leaning against the sewer wall in support while breathing heavily. The swim downriver had been exceptionally easier than the day before, but between yesterday's upriver marathon and this morning's challenging… experience… He was at his limit. In his exhausted state, there was no way he could continue, let alone face the army of alien robots awaiting us at home. That didn't mean Leo wouldn't be stupid about it, "Come on bro, you got to rest. There's no way you're going to make it there today."

Leo's mouth formed a tight line, "I don't have the luxury of rest. Every second we waste is a second Mike and Don don't have!"

"Don't you think I know that? I fought those things too remember?" he raised an eye ridge at me, "_Before_ I transformed, idiot! But in case you haven't noticed I am no longer gamera-sized and as much as I hate to admit it, I can't take those tin cans alone."

It was true. Since this morning's "events" I had remained my normal handsome self. Well almost normal. I still had these weird sensations occasionally run through my scales like they were trying to shift in place, but I hadn't mentioned it to Leo. He was so happy to have me back that I didn't want to burst his bubble. Besides, he had enough to worry about already. I didn't want to add the threat of me having a relapse to the list. Once we rescued our brothers, I would get Donnie to check things over for me. Hopefully, my body was now mutagen free and these sensations were just a side-effect from the last transformation that in time would disappear. Hopefully.

Leo, ignoring me, inched himself along the wall trying and failing to hide his pain. I grabbed him by the arm, "Look Leo, you can move along like this all night and still not get to the lair by morning or you can rest now and after a few hours of sleep we book to the lair in no time flat."

He turned to me, eyes filled with worry, and then slumped down onto the damp stone and held his head in his hands, "Why did this have to happen now? The one time I couldn't be there? Is the universe purposely trying to rub it in my face that I can't be in two places at once?"

I sank down beside him, "I think that's exactly what the universe is trying to tell you, Fearless. As much as you try you're only one turtle Leo. I know it's cliché, but all you really can do is try your best. Sometimes though you gotta make hard decisions based on who has the most need. You knew I needed you more than Mikey and Don did. Trust me, you're not giving them enough credit; they really can take care of themselves. Me on the other hand, well I don't think things would have turned out so good if you hadn't be there."

He lifted his head up slightly and I hoped he could see that I had meant what I said. I hissed in pain as a tremor suddenly went through my outstretched leg. I grabbed it before Leo could see the shifting scales. He jumped in concern, "Raph you ok?"

I massaged my leg and the scales settled just as quickly as the pain had come. I knew Leo did not have the energy to deal with this right now. I continued to stare at my calf as I massaged it hoping to make the lie convincing, "Yeah, just a muscle spasm." I looked up and shrugged, "Guess you're not the only one who's beat."

He seemed to buy it and closed his eyes as he leaned back against the wall. "I guess we really do need to rest a bit."

I snorted partly in victory and partly in relief that he missed my lie, "Maybe that's why I've been after you the last twenty minutes to give it up. You know, just cuz you're the Leader doesn't mean the rest of us can't order you around once in a while. How's it go "an officer physically unfit for command" or something along those lines?"

He laughed, "Well technically our chief medically officer would need physical evidence to support your claim. So without Donatello here I reject your claim. It doesn't matter though, because last time I checked _Star Trek_ is fiction – not reality."

I rolled my eyes and grunted, "Says the mutant turtle to the other mutant turtle while contemplating how to take on robot aliens with ninjutsu. Yeah our lives are totally the same as _Real Housewives_."

We both laughed at that, but finally Leo appeared to admit defeat by curling up on the floor, "Well when you put it like that of course it sounds ridiculous. Take first watch for me?"

I smiled into the darkness, "Course."


	2. Chapter 2

Chapter 2

The sewer tunnels were quiet. The only sounds that penetrated the semi-darkness was the flow of water and the gentle rhythm of Leo's sleeping breaths. I was thankful for the lack of intruders – I had bigger problems. As Leo slept, my body continued to have episodes (or for lack of a better word, tremors). An area of flesh would briefly distort and then become smooth again. I was now almost convinced that the mutagen was still in my system. I silently sighed. The only real victory of the day was conquering that nightmarish manifestation of my anger. I was still my usual cantankerous self, but I felt no sign of that dark presence. Even if I did, there was no way in hell I would let it physically manifest again, which actually would be pretty easy since as soon as my mind had decided to be back in control it was. That dark anger needed me, but I sure as hell didn't need it.

As Leo slept, I kept trying in vain to come up with some kind of strategy to save our brothers. Leo and I needed to first gather further information on Don and Mike's situation. Leo would have tried to reach them with his shell cell, but the phone got totalled by Nightmare Me. I, unsurprisingly, had not brought my phone so now my elder brother and I had to personally gather intel. However, even if we were lucky enough to find our brothers in the lair, it would still be next to impossible to save them. Those robots were insanely tough. If I hadn't gone all "Raphzilla," as Mikey fondly put it, we would have been cooked. I doubted that even if these tremors led to another transformation that it would yield that same form. So it came down to Leo and I pushing our ninja skills to their limit in order to save our brothers. Leo hadn't said it, but we both knew the odds were stacked against us.

I was beyond antsy just sitting there staring into the darkness with nothing to show for my ruminations. Abruptly, I stood up and decided to go scope out the tunnel a little bit. Leo was not obviously detectable – hidden in a depression in the wall of the tunnel – but I still wouldn't go far. My remaining sai was sheathed in a spare belt Leo had brought with him. I was more than ready to pull it out at a moment's notice. I was always itching for a good brawl. There was no better release that pushing oneself to their limits in order to just survive. Battle gave me a sense of accomplishment and purpose like nothing else could. It made me feel _alive_. As I moved down the tunnel, I had no doubt that my battle rush would be more than ample in our impending robot brawl. The uncertainty of the battle's outcome could only fuel that fire.

I walked around a bend in the tunnel to find a large dead-end chamber connected to the main sewer passage. A fuse box was on the far brick wall. Fuse boxes littered the sewers as a way for simple and easy electrical access when workers had to do scheduled maintenance. Donatello also loved them. He was always plugging into them to mess around with the lair's electricity. He switched our lair's source of juice regularly so that the power companies wouldn't question why a certain part of the sewer continually used far more energy than the rest of the city's plumbing. It wasn't like we could just sign up as residents of the city to get power like the humans. So Don kept them off our trail with the help of the fuse boxes.

Thinking about Donnie's ease of manipulating the power companies' own system against them couldn't help but make me more anxious. I had played it cool so I could convince my stubborn brother to finally rest for a bit, but inside I was quaking. I couldn't bear for anything bad to happen to Don and Mike and I was seriously worried about what those robots would do to them. It would be all my fault too. If I had for once in my life been a little less impulsive, we would now not be the target of the TCRI robots' attention. We barely made it out alive last time and that was only because…. _Because I turned into that..._

I shook my head trying to clear the memory of looking at my reflection while in that form, but it instead switched to the memory of me towering over my brothers, which was replaced by the memory of me making steel confetti out of that tank, which was followed by another vivid memory and then another. I couldn't seem to distract my mind from the waves of my Raphzilla memories. In desperation, I tried to concentrate on examining the space I was in, but my focus was abruptly shattered as a massive wave of tremors overtook my body. I fell to my knees watching in horror as my skin bubbled and shifted before my eyes. I gasped in pain as I saw my bones lengthen and my muscles stretch. I felt my belt snap as my abdomen enlarged. My sai hit the ground with a metallic ring. I held the sides of my head desperately trying to somehow stop what was happening; I was all too aware of my nails digging into my skull as they too changed. A voice came from behind me, "Raphael?"

Leo probably instinctively woke up the instant he heard my sai hit the floor. I couldn't move to look at my brother. My body was on fire with the grinding and distortion of bone and flesh. My eyes watered from the pain. I barely even registered Leo's footsteps as he moved around to face me. The pain dissipated and through my moisture-filled eyes I was all too aware of a familiar sensation – once again I loomed over my brother. My flesh slowly stopped pulsing and I knelt there undoubtedly back to my Raphzilla self. I groaned, my voice significantly deeper, "Ya gotta me kidding me…"

Leo looked up at me in shock, "But…. But I thought you were back to normal?"

I grunted, "I was! Apparently it wasn't permanent!" I was beginning to feel thoroughly pissed, but when a thought occurred to me, my anger started to abate, "Hey Leo, I know this is kind of sucky, but at least its timing was good."

Leo frowned unimpressed, "Are you serious? Its timing couldn't have been worse! We don't have time to deal with this!"

"You're not thinking Leo. We have one hell of a battle coming up and until a moment ago I was just thinking about how badly the odds were stacked against us. But now," I tapped my huge black plastron, "we have a heavy weight on our side."

Leo crossed his arms on his chest still frowning, "Maybe so Raph, but your transformations are becoming more irregular. I'm worried about how unstable your body is becoming. I'd really rather have Donnie-"

I cut in growling, "You're forgetting that said brainiac turtle is currently unavailable to give any input Leo. We kind of need to save him before we can attempt to fix this."

Leo hissed in exasperation, "Don't you think I know that?"

I cocked an eye ridge at him. Leo let out a sigh of defeat, "Sorry Raph. I'm just a little stressed here and to be honest I feel a bit like a kid who was given his Christmas presents only to have them taken away the next morning. I… I was just so relieved and _happy_ to have you back to normal."

A stab of pain went through me. I felt much like Leo. Yeah this was convenient, but I was incredibly relieved and frankly ecstatic to be five feet tall again. I liked my old body. I spent my life sculpting it to reflect myself. It was _mine_. Now that I was back in this unfamiliar shell… Well it made me more than a little depressed. "Leo, I-"

Then yet another massive wave of tremors went through me. Admittedly, less painful that before but still hardly pleasant. I cursed, "Shit… Not…. Again…."

Within moments of experiencing the same tremors (of not even five minutes ago) I found myself back on eye level with Leo, who was looking more confused than ever. I lifted up a hand to examine it, "What the fuck? What the hell is going on?"

Leo only continued to stare, apparently too shocked to speak. I rubbed my aching limbs, "When is this fucking mutagen stuff gonna make up its fucking mind? This is getting fucking ridiculous!"

Leo seemed to regain some of his composure and folded his arms in thought, "Hey Raph, what were you thinking about a moment ago."

I snapped in irritation, "Weren't you fucking listening at all? I pretty much voiced my fucking displeasure. Fucking damn it!"

Leo pinched the bridge of his nose, "No stupid. I wasn't asking about what you thought after the transformation, but before. I'm not that stupid that I can't decipher your colourful language Raphael."

I grunted in response. Folding my arms on my chest, I looked down in thought. I examined my comparatively small feet (secretly relieved that they too were again normal) and mumbled, "I was just thinking how much I liked my old body – you know this one. How I worked so hard to make it my own and-"

Leo's eyes looked abnormally bright and cut me off in a tone of understanding, "I know this is going to sound weird Raph, but just try it ok?"

I raised an eye ridge, "You thinking dirty thoughts again Leo?"

He glared in response, "Please just keep your mind out of the gutter for five minutes ok! Now close your eyes."

"Leo…"

"Just do it!"

I cursed under my breath, pissed he wasn't explaining this new found revelation of his. I accepted when Don knew more than me, it was the nature of the beast, but I couldn't stand not being in the loop when it came to Leo. Still, I begrudgingly did as he asked. "Now think about what I look like."

I snapped my eyes open, "What?"

He sighed, "Raphael for once in your life just trust me!"

That touched a nerve that was a little too fresh so I obediently closed my eyes without further complaint. He spoke more calmly, "Now focus all your attention on drawing a mental image of me. Think of every detail. From the colour of my eyes to the shell on my back."

It wasn't a difficult thing to do. I knew what my brothers looked like better than I knew myself. I had spent almost every waking moment of my life with them. A clear image of Leo was in my mind before he even told me to focus. Then it happened. Another violent tremor went through my body and I once again found myself on the floor. I squeezed my eyes shut willing the pain to end. After a few moments I opened my eyes in relief as the pain edged away. Leo expelled a breath. I groaned, "What now? What hideous thing have I turned into now?"

Leo startled me by laughing. I snarled in confusion and embarrassment, "What the hell is so damn funny?"

He just continued to laugh as he pulled me to my feet and guided me to the water moving through the main tunnel. Finally he stopped laughing long enough to point at our reflections and say, "Right now I'd watch those insults bro. Take a look."

I faced my reflection and grabbed Leo's arm in support. There looking back at us, were two identical copies of Leonardo.


	3. Chapter 3

Chapter 3

I was so shocked I wasn't even remotely embarrassed by my vice-like grip that now held Leo's arm. There they were: two Leonardos. One looking more than a little too pleased with himself and the other gaping stupidly. I quickly closed my mouth to see said Leonardo close his mouth. I released my brother's arm to see the same Leonardo mimic the movement. I was a perfect duplicate. The ice blue eyes, the slightly lighter skin tone, even his signature katana and blue mask matched flawlessly. I finally tore my eyes away from the water to now examine the tangible body in front of me. I had Leo's strong, yet slightly more slender arms and legs, his calloused hands, every physical feature I knew absolutely and undoubtedly were Leonardo's now belonged to me. I eventually found my voice only to find that it was also Leonardo's, "What. The. Hell."

If I wasn't so catatonic I probably would have laughed at the sound of Leonardo swearing in such vehemence. My brother laughed and I snapped, "What is _wrong_ with you?"

He stopped laughing but still smiled, "It all makes sense now! I can't believe it took me so long to figure it out!"

My patience was at an end, "WELL DON'T BOTHER YOUSELF ENLIGHTENING ME WITH THIS NEW FOUND KNOWLEDGE OF YOURS! I'D HATE FOR YOU TO HURT YOURSELF!"

I couldn't help but storm away from him. I returned to the fuse box chamber to retrieve my sai and the remnants of my belt. I felt his presence behind me and whirled around, my sai meeting his katana. Even as exhausted as he was, Leo was not surprised easily. "Calm down Raph! It's not like I've been intentionally leaving you out! I just thought it'd be obvious by now. How about you stop and think for a minute?"

I didn't budge, "How about you stop playing the "you only learn from the lessons you learn yourself" crap and just spit it out already?"

Leonardo was not so easily cowed. "Or how about my dear hot-headed brother who wears a red bandana and loves his sai more than life itself, who has slightly darker green skin than me, who may be about my height but is physically stronger than me, who is thicker set than me, who shares a similar shell, who has amber eyes, who has more than his own fair share of scars, who..."

He raised his eye ridges expectantly at me and it finally clicked. I took a deep breath and let the words from his continuous commentary flow over me. It still hurt and I still couldn't stand while it happened, but somehow it was getting easier. I opened my eyes and was back to myself. I, Raphael, stood up and looked at a now silent, but grinning Leonardo, "Touché Fearless."


	4. Chapter 4

Chapter 4

We were almost at the lair and after the long walk I still had no idea how to view this "ability." My whole life I had been an outsider. Watching the world above from the sewer shadows had left me longing to know what it would be like to roam with the humans. To just be another unremarkable face in the crowd. Even amongst my fellow terrapin brothers, I had felt always a little too different, or until recently anyway. Leo had reminded me of the love my brothers had for me then and still had for me now. It was not my brothers who distanced themselves from me, but I who sought isolation. When we swam back to the city after this huge realization, I found myself excited to see my brothers. I felt like I had been given a second chance. I was content knowing that even if I would still never belong to the human world I would always have my brothers. That's what I had thought until I discovered I could shape-shift. Now I had no clue what to think.

Before we continued to the lair Leo had insisted that I try a few more shapes to see the level of control I had. Not only could I transform into each of my brothers, but I could also turn into whatever form I desired. That included human. It was when I stared into the amber eyes of a young teenage human male that I abruptly changed back to normal and told Leo I had enough. Frankly, seeing that human face that so resembled my reptilian form had scared me – it was reality smacking me in the face. Yes, now I could take whatever form I pleased, but by doing that I still wouldn't ever actually "be" a human.

Even worse, shape-shifting risked my relationship to my brothers. It was all too evident that my emotions played a role in my transformations. Anger especially fueled unexpected changes. That was a threat enough to my family, but there was another dark thought that plagued my mind. I could now enter the human world, but my brothers could never follow. A new feeling of isolation settled over my heart as I came to this realization. I had always wanted to know what it was like to live amongst the humans, but these dreams always included my brothers. It seemed absurdly cruel that only one of the four of us had been granted such a boon. The more I thought about it, the more I wanted nothing to do with it.

As we approached the secret vent entrance we would use to sneak into the lair, I made my decision. I had to keep this a secret. Leo would always know, but of all my brothers I knew he would understand the best. This secret would never leave the two of us if I asked it of him. Leo wrestled off the grate from the wall and I tentatively made my request, "Leo?"

He lay the grate carefully on the ground and then looked at me curiously. Besides speaking of our plan we had talked little on our trek. Both of us were deep in thought, "Yeah Raph?"

"I know this is asking a lot, but uh can you not tell the others about this?"

I folded my arms nervously. Even though I knew he'd say yes, this whole shape-shifting thing made me uncomfortable. I just wanted to be normal damn it! Well as normal as a teenage mutant ninja turtle could be anyway. Leo however, was the epitome of calm, "You mean the shape-shifting thing don't you?"

I nodded and mumbled, "Yeah…"

He raised an eye ridge, "You don't have to be ashamed of this Raph."

I narrowed my eyes, I didn't want an "it's ok to be yourself lecture" from big bro. I just didn't want to ruin this second chance. I didn't know how to explain that to Leo though. Expressing myself through words had never been my strong point. "I know that Leo! Geez why is it always a lecture with you?"

He frowned and I briefly saw a look of hurt go through his eyes. I felt as stab of guilt and stumbled on, "Man… Sorry I didn't mean it like that Leo. Look I'm just a little freaked out ok."

His eyes softened with the apology, but he still looked concerned, "I understand Raph, but you don't have to shoulder this alone. Talking about it might help."

I sighed, "Maybe, but I need some time to figure this out. Please Leo?"

He scratched his head thoughtfully, "Alright I won't mention it to anyone, but once you figure this out you really should tell the others. Besides what am I going to tell them when they see you back to normal?"

That was a legitimate question. "Just uh…. Just that the second mutation amazingly enough turned me back to normal? Don himself did say he had no idea what I would turn into…"

Leo rolled his eyes, "You and me both know he won't buy that. Plus, he's going to be all over you for a blood sample to check for any remaining mutagen. Somehow I feel like he'll see something that's definitely not kosher."

I waved him off, "Don't worry about that bro. If we both keep to the same story we should deflect too many questions and when he goes for blood I'll just tell him to piss off. If you back me up he'll leave me alone. He always listens to you."

Leo shook his head and proceeded to the vent. "I'll do my best, but I still don't think this will work."

I crawled into the vent behind Leo in silence. I knew Don probably wouldn't buy it either, but I just needed some more time. I'd tell them when I was ready. _If I'm ever ready_.

I quickly shook those thoughts away. I could figure out the details later. Right now, we had our brothers to save.


	5. Chapter 5

Chapter 5

We moved silently and quickly through the vents. This was the only way into the lair besides the sewer and elevator entrances and we could not risk getting caught. Before we had gotten too far Leo flipped open a hidden keypad and typed in a series of digits. The small flashing green light on the pad indicated that the vent's security was temporarily disabled. As long as we kept quiet, we would be in the lair in no time and hopefully undetected. Within minutes, we found ourselves at the vent's exit that lay above the second floor near Leo's bedroom. Leo moved ahead so that we each could look through the grate and inspect the lair. We were not prepared for what we saw.

First, we saw Mikey at the entertainment center munching popcorn and watching some bad slasher flick. Next we saw Don leaving the kitchen with a fresh cup of coffee in one hand and a cup of tea in the other. What made both Leo and I exchange bewildered glances was the sight of a giant rat kneeling upon a bamboo mat by the pool in the center of the lair. Splinter was alive!

It seemed too good to be true, but as we scanned the lair again we still saw no signs of alien robots. I looked at Leo again as to what we should do when a voice spoke, "Ah thank-you Donatello this is just what I need before I meditate, but first I have a question."

Don replied, "Yes Sensi?"

Splinter closed his eyes and sipped his tea, "Why are Leonardo and Raphael entering the lair through the air vent? Are the other entrances damaged?"

Don looked up in astonishment while Master Splinter smiled knowingly. Leo and I could not help grin from ear to ear as we opened the grate and jumped down into our home. We were at Master Splinter's side before he could take another sip. We cried in unison, "Master Splinter!"

The rat, our Father, placed his tea on the ground nearby to meet our embraces. "Ah, it is good to see you my sons!"

Leo was the first to speak, "What? How? When did you get back Sensi?"

Master Splinter released us, "It seems we both have stories to share. Just as you were not expecting my presence, I have to admit I was not expecting to see Raphael in his present state."

I looked quizzically at him, "Sensi…"

He gestured to Don, "Donatello told me you had been changed rather… dramatically, but it appears you are free of this ailment?"

Leo looked pointedly at me, but Don and Splinter were unaware since they too stared at me. I looked down not wanting to meet their eyes, "I did mutate again as Donatello predicted Sensi."

Don's jaw dropped, "And just like that you mutated back to your normal self? Based on your dramatic cellular modifications I would have never-"

Don was getting to close to the mark. It was time for an intervention. I waved Don off and gave him my most exasperated voice, "As fascinating as it is to hear you geek out about this Don, I really don't care how it happened." I threw in a bit of swagger to further my point, "I am just glad to be my usual handsome self."

Don opened his mouth, but I ignored him and turned to the rat beside me, "What I do want to know is are you ok Master Splinter? We were ready to pull off our shells worrying about you! Where were you all this time?"

Leo thankfully supported my change of subject, "And where are those alien robots Mike was talking about? We expected to return to… well, chaos."

Master Splinter regarded Leo shrewdly, "Does this disappoint you Leonardo?"

Leo raised his hands shaking his head, "No! Of course not Sensi. I am just surprised and confused. Happily surprised and happily confused, but surprised and confused all the same."

By this point, Michelangelo had casually walked into the scene, his arms crossed behind his head, "Bros, you're back!"

Leo, obviously nervous about keeping the heat off of me, pounced on Mike, "Mikey, tell them!"

"Tell them what dude?"

Leo frowned at his youngest brother, "Michelangelo, this isn't the time to mess around! Where are the aliens, the robots, the battle wounds? You know, all the stuff you talked about on the phone!"

Mike looked slightly bewildered before a light of understanding entered his eyes, "Oh that call! Dude I was totally telling you about our awesome Utrom buddies! Didn't you listen to a thing I said? Sensi was with them all along! They fixed him up and everything. Also crazy story: they're the same guys who mutated us! Well the ooze from their trans-thingy did but you get the idea."

Don jumped in next, "It's called a transmat Mikey. Thankfully they are familiar with the mutating agent and so they offered to take a look at Raph for us. They thought they may be able to reverse his new mutation." He ran his eyes over me, "Apparently that's no longer the case but I'd still like them to take a look."

I felt my temper boiling. Were they serious? Those were the same guys who were ready to destroy us a few days ago! And they mutated me! I had this whole shape-shifting problem because of them, "Are you nuts? There's no way I'm letting those alien scum experiment on me. I'm glad we have Sensi back, but we should be avoiding these guys!"

Leo also seemed skeptical, "Raph is right, they were pretty aggressive at the warehouse."

Master Splinter raised his hand to silence our displeasure. I ground my teeth in frustration and attempted to swallow my anger. I instead felt a tremor run through my left calf. _Shit. Keep it together Raphael. Don't let it control you_.

I briefly closed my eyes and released an exasperated breath. I felt another tiny tremor in the same place, but thankfully the skin slowly stilled. I forced my focus to Splinter, "Leonardo, Raphael, your brothers speak the truth. These aliens are our allies. While I healed I spent much time with these beings learning of their culture and of their world. They are truly peaceful souls. From my understanding, what occurred at the warehouse began as a misunderstanding –" he paused to look directly into my eyes. I bowed my head in shame, "– that unexpectedly turned to disaster. The workers would have never attacked you to begin with, but you, Raphael, attacked first. When they thought you were a hostile alien due to your reptilian appearance they acted accordingly. Sadly, after you mutated, they found themselves fighting not just in defense, but in a desperate attempt to survive. Considering the damage your rash actions have caused, it is a testament to these beings' peaceful nature that they have not sought compensation. Instead they have extended an olive branch to us by trying to reverse any damage you may have sustained from your exposure to the mutagen. You may now appear normal –" another agonizing pause, "–But I know their offer will still stand regardless of your appearance. Therefore, the least you can do is provide them with the utmost in courtesy and accept their kindness."

I stared bullets into the floor with my eyes. The resentment at Splinter's rush to defend these aliens – good or not – along with his penetrating stare only caused more tremors to rush through my skin. I had to keep it together. He knew I was hiding something, but I refused to let him know the nature behind my secret. Especially now that I knew how disappointed Splinter was in my actions at the warehouse. The last thing I wanted was to change now and provide him with further evidence of my royal screw up. I mumbled, "Sorry Sensi."

Splinter responded, "Although I will not deny my disappointment that you have yet to learn to restrain your impulses Raphael; I am not the one who deserves your apology. You shall demonstrate your remorse when we visit the Utroms tonight."

My heart skipped a beat and a tremor ran through the back of my neck. I felt utterly trapped. I wanted Splinter's forgiveness, but the only way I could hope to earn it was by facing the Utroms. If Don could figure out my body wasn't back to normal these space freaks would definitely figure it out. My secret would be known and I just couldn't bear the thought of what my Father would think of me then. "But Sensi-"

Splinter cut me off with a deadly edge in his voice, "Raphael have you no honour? Do you not realize how many Utrom lives were lost that night? How much sorrow you have caused from your rampage? A rampage that would have never occurred if you did not allow your rashness to control you! Did you not pay any attention to what I have tried to teach you all these years? Because your unwillingness to accept responsibility for what has happened is leading me to believe that I was wasting my time."

Silence. Leo, Don, and Mike appeared frozen in shock at our Sensi's statement. My breath caught in my chest and I felt the tremors worsen. Did Father not realize how badly I felt about this? Did he not know how I was willing to isolate myself for the rest of my miserable life if it meant my mutated form would cause no further harm? I wanted nothing more than forgiveness for this! Did Father really believe I was such a failure? Such a disappointment? Where had I gone so wrong? Did he not realize everything I did I did for them? That I would do anything to protect my family? I desperately wanted to tell them the truth but how could I?

I wanted to say something, anything to try and make him understand but the tremors were now alarmingly strong. I was out of time. My skin was starting to stretch and like the fuck up I was, I bolted. I slammed my bedroom door and managed to lock it just before the tremors took over – feeding off my sorrow. I tried to focus on my true body as Leo had told me, but my heart was screaming. My Father thought I was a monster. A lost cause. I began to succumb to the pain, but a glimmer of memory halted my progress. The image of two Leonardo's one younger and one older staring into water seeped into the corners of my mind. They were slow at first, but I forced my mind to focus on them. Soon the memory flooded my mind and I knew even if Splinter hated me, I still had my brothers. I still had Leonardo.

Finally the tremors stopped and I cracked my eyes open to examine the damage. I didn't grow as much as before, but I still almost doubled in size. I also succeeded in not growing a tail or having my shell change colour, but my muscles were way more beefy and I was in need of a serious nail-trimming. I wasn't pleased about being almost eight feet tall, but at least I looked more or less the same. I had still managed to retain what my brothers' saw in me even when I couldn't see it myself.

I collapsed onto my knees drained. I wasn't willing to try changing again until I recovered. I would probably make it worse by trying to go back to normal now. Instead, I grabbed the pillow from my hammock and laid back on the rug beside it. My eyes fixed on the ceiling as I folded my arms behind my head between the pillow and the floor all too aware of how small my pillow was. I figured I had at least a few hours before I walked the green mile and confronted Splinter. I knew I had to face the Utroms and risk them revealing my secret, but I refused to let them force a wedge between me and my family.

I ground my teeth in frustration that things had turned out so poorly. I had never imagined Sensi's homecoming to be like this. It was supposed to be a joyful event not one filled with anger and shame. Definitely not one where I was the source of Sensi's displeasure. I could not help but feel a twinge of rage at the unfairness of it all and was rewarded with another tremor through my arms that caused my head to rise an inch as my biceps and deltoids increased in girth. I cursed under my breath and was about to unleash my wrath on my pillow when a soft knock came from the door. I glared at the wood separating me from the hallway. The last thing I needed right now was visitors. I barked at the door praying that the door disguised my deeper voice, "Piss off!"

"Open up Raph."

I ran off a few more curses as I got up, ripped the door open, and scowled down at Leonardo.

**A/N Some of you may think Splinter came off a bit harsh here and I kinda agreed at first until I chewed it over. **

**If you really think about it from Splinter's perspective it's not actually that bad. He was critically injured and the Utroms were the ones that saved him. He then spent several months living with them while he recovered and undoubtedly got to know them quite well and even view them as a kind of second family. Then many of the Utroms that were in the warehouse that day were killed, Splinter lost many of his friends. To know that his own flesh and blood was the one who caused so much pain alone would have been incredibly hard to cope with, but then when Raph's bad communication skills came across as apathetic… well Splinter kind of snapped. **

**Too often I think we forget that Splinter is not perfect and he has feelings and emotional needs just like the rest of us. This was simply one of those instances. **

**Anyway sorry for the long rant haha. I hope those who stuck with this are still enjoying it! **


	6. Chapter 6

Chapter 6

**A/N I just realized how heavy part 3 has been on Raph POV's… Whoops… Anyways this is the last chapter of this arc and then I'll have brief epilogue and that will be it. Don't worry I still have plans for some one-shots and some other stories in this universe I've developed, but they will probably take place in the future by at least a few years. **

**Now without further ado…**

It was a testament to the level of trust Raphael and I now shared that he had opened the door without asking if I was alone. Of course I ensured I was alone since I knew he had transformed due to his abrupt departure, but I still felt touched by his assumption.

The Raphael that greeted me at the door was a new model. He looked essentially the same as before with the addition of at least three feet in height and muscles that screamed steroids. He practically threw me into the room before slamming the door and locking it. He regarded the door for a moment before dragging his weight rack against it. He probably wanted to ensure no one would disturb us, which was a now guarantee since that thing had to be near a thousand pounds. When he turned to me without any sign of fatigue, I was yet again awed by the strength he could now muster. Raph didn't miss a beat as my eyes smoothly slid to the weights then to him, "If you're gonna gawk you can piss off Leo."

I raised my hands in peace at his murderous growl, "Stop telling me to "piss off" Raph! I'm doing my best, but it is going to take me some time to adjust. So just try to chill ok."

He snorted darkly as he eased his massive bulk into his hammock. It sank alarmingly low, "How do you think I feel?"

I opted to avoid the strained hammock and leaned against the opposing wall. "Why didn't you change back already then?"

This was met by an explosion. In an instant I found my volatile brother inches from me. He placed clenched fists onto the wall on either side of my head and I was forced to look up to meet his eyes since he refused to relinquish any height. He hissed in a dangerously quiet voice, "Don't you think I would if I could?"

His tactics were typical. He used his physical presence to try and manipulate me. I quickly smothered my own spike of anger at this attempt at intimidation. I knew he was hurting and was undoubtedly struggling to cope. Raphael had more than enough self-hatred on his own. I could only fathom its new level of instability after Splinter's unexpected outburst. Raph had made an unbelievable amount of progress over the last few days, but he still had a lifetime of habits to change. So I figured it was best to treat him the same way I always did when he was like this. I needed to remain calm and show nothing but confidence.

Continuing to casually lean against the wall, I met his gaze, and held it. After I minute I raised an eye ridge and prayed he would back down. He briefly closed his eyes and expelled a hot breath before stepping away while pinching the bridge of his nose. He then abruptly turned and I calmly said, "You just need to rest a bit then you can go back to normal."

His hands came down to his sides in fists but his carapace continued to face me. Nonetheless, I patiently waited for a reply. A few minutes passed and he still had his back to me. I silently slipped from the wall and came up behind him. In a brotherly attempt at humour to relieve the awkward silence I placed my hand on his shell and joked, "Hey, since when do you give me the silent treatment? I thought that was reserved for Mikey."

The instant I touched his hard carapace I felt him shaking, but the motion was distinctly different than his prelude before transforming. I caught sight of his face before he turned away, but I knew he wasn't giving me the silent treatment. Raphael was crying. His cheeks had distinct tear-stained trails that were continually refreshed by new tears. Yet, he still had a degree of control by remaining silent. I slid my hand to his hulking arm, "Raph…"

And he lost it. A heart-wrenching sob escaped his chest and he sank to his knees. His hands covered his face as a last ditch attempt to hide this display of raw emotion, but he could not hide his audible sorrow. I was frozen in shock.

I had not seen Raphael cry since we were kids. Even then, they were always the kind of tears children tend to produce. Shed over petty incidents such as the loss of a toy or the skinning of a knee. What I was witnessing now was nothing like those and was completely foreign to me. I had often soothed such sorrows in Michelangelo and occasionally in Donatello, but never in Raphael. Usually when he was upset we'd hit the dojo, spar, and then when we eventually collapsed in exhaustion Raphael was good to go. Looking at him now I knew sparring just wasn't going to cut it.

I remembered how to work my legs, sunk down beside him, and then approached him as I would Michelangelo. I stroked the back of his shell and hugged his side. This was usually the part where Mikey would cuddle into me and sob against my plastron while I rested my chin on his head, but I was unsure how Raph would react. He froze briefly and then turned to lean his face onto my shoulder. I adjusted to try and accommodate his weight. Sensing this, he put his hands on the ground on either side of me to alleviate me of the majority of his bulk, but he kept his head tucked between my shoulder and neck. Thankful for this gesture, I returned it by wrapping my arms as far as they would go around him. With my left hand I managed to find one of the grooves in his carapace and used my thumb to rub up and down it. This always helped Donnie and I knew it was helping Raph as I felt his body relax a little more.

We stayed like that for a while and eventually Raph's sobs eased enough to choke out, "I… I… can't do it."

I pulled my right hand towards me and set it to work rubbing the back of his neck, "Do what Raph?"

"See those… those aliens… the Utroms…"

I stayed silent knowing there was more, "They'll know for sure."

"Know what Raph?"

He pulled away and looked at me thoroughly disgruntled. He waved his massive arms, "That I'm like this Leo!"

Right that. I inwardly cursed myself at my stupidity. If I was going to help Raph I was going to have to do a better job of staying on his thought train. "They just want to help you."

He shook his head and appeared to momentarily regain his composure, "It's not them that's the problem Leo! It's Splinter!"

He covered his face again as another wave of sobs escaped. I desperately shifted through the last few hours trying to piece together my distraught brother's thoughts. Then I remembered what he said before we entered the vent leading to the lair and it clicked. "Raphael are you worried he'll hate you if he knows you can shape-shift?"

His watery amber eyes met mine and I knew I was back on the right track, "You heard him Leo. He already hates me for what happened at the warehouse. If he knows about this my presence alone will be a constant reminder of how I screwed up. He'll look at me and know that at any instant I can change into that same monster that killed those Utroms!"

I shook my head, "You're wrong Raph. You will never turn into that monster again. I know you won't let it happen. Just think of the progress you've made already. You are more distressed than I've seen you in years and you still managed to grow only three feet. That's way better than twenty and even when if you wanted to change into that form I know you'll stay in control. You finally faced your demons when you brought down that nightmare and now you get to decide what happens next."

He had finally stopped crying, "You really think it's gone Leo?"

I placed my hand on his, "I do Raph."

"And that I'll get control of my changes?"

I nodded again, "You're already getting the hang of it. You know these Utrom guys might be able to help. If they understand this as well as Don says."

"I still don't want the others knowing Leo."

"Well then you need to talk to these Utroms more than ever. You're going to need to master this as fast as you can if you want to keep it a secret."

He exhaled and his face now held an air of determination, "I'm going to tell Father that I'm going, but I'm going to do this right. I'll tell him you all can come, but when the Utroms go to examine me I want to go alone so I can apologize alone. It'll help show that I trust them and that I really do want to make amends. Hopefully that will also give me an opportunity to convince them not to tell the others about this."

He stood up and offered me a hand, "That's actually not a bad idea Raph. Hits two birds with one stone," I looked him over, "you might want to get cleaned up before you go out though."

A sheepish grin crossed his face as he pulled the weight rack away from the door. "What no jokes about my waterworks?"

I grinned, "Naw, I'm just going to blackmail you with it. Next time you eat my Pop Tarts I'm regaling Mikey with all the details. Then the real torture begins."

We exchanged glances undoubtedly sharing similar apocalyptic visions of what Michelangelo would do with that kind of information. "Jerk."

I felt myself smirk, "You don't see me denying it. What can I say? I take my Pop Tart addiction seriously."

Raph grinned as he closed his eyes and furrowed his brow in concentration. Within moments he was eye level again and had managed to remove any sign of tears. I turned to leave and felt him grasp the back of my shell. I turned to be engulfed Raph's arms. I savoured the loving display of affection from my brother. I knew the raw emotional displays I witnessed lately were rare events that would not be seen again for many years to come. We parted and our eyes met with understanding. We had no need for words.

**A/N All the feels! Ok maybe I went a bit too far with Raph here, but come on. If you're father, hero, and idol told you that you essentially had failed at life you'd be pretty upset too. Add in the stress and exhaustion from the last few days and most would probably crack. I also really wanted to show that Part 2's events really did have an effect on Raph and that he is really trying to change. Thus this moment of brotherly love.**


	7. Epilogue

Epilogue

As per Splinter's request, Raphael accompanied his brothers to the Utrom-operated TCRI building. Of course turtle luck was true to form and after accidently transporting themselves across the galaxy the turtles found themselves in the middle of a war between the Federation and the Triceraton Republic. The turtles did eventually make it back, the Utroms finally returned to their home world, Master Splinter forgave Raphael, and the mutant rat apologized to his son for judging him so harshly. Splinter assured his son that he would always love him and would always be proud of him.

Before the Utroms left they thoroughly examined Raphael to announce to the red-clad turtle's dismay that his condition was permanent. The mutagen had somehow managed to manipulate the turtle's DNA so that his cells were constantly synthesizing more of the agent. Due to the variable nature of the substance, in order to stay in control of his transformations, Raphael had to shape-shift daily.

Thankfully, the Utroms understood Raphael's desire for privacy and revealed nothing to the family assuring them that Raphael was currently fine (which he was since he had changed just previous to that particular conversation). With the help from Leonardo, Raphael slowly gained control over his ability. After much training and a great deal of patience he was able to easily shift to any form he desired.

This of course included becoming human. However, although Raphael could move freely among the citizens of New York he chose not to. He felt that he was a walking deception and that greatly troubled him. Even when he looked in the mirror to see a perfect human returning his stare, he knew that under that layer of flesh he was still a mutant turtle and he felt that the humans would always secretly wonder if he was truly one of them. Raphael believed no amount of shape-shifting could ever change that, but there was a more another factor in his decision.

Raphael did not want to enter the human world without his brothers beside him. The red-clad turtle had indeed been given a second chance to mend the bond with his brothers. After the Utroms departed, that bond grew and he cherished it more than anything. Leaving his brothers to live with humans would fracture that bond and ever his brothers' protector, he refused to submit his brothers to such pain. He did not want his ability to ever drive them apart.

Leonardo, true to his word, did not tell the others. When Donatello or Michelangelo questioned their eldest brother about what happened the day he chased after Raphael, their leader always pleaded ignorant. Leonardo knew that was Raphael's story to tell and he would when he was ready. Until that day arrived and as long as Raphael was content to fight alongside his brothers as a teenage mutant ninja turtle Leonardo would keep his silence.

Fin

**A/N So that's all folks! Well sort of. Like I said earlier I intend on writing in this universe some more, but this arc is done. Thank-you for reading and I really hope you enjoyed it!**

**If you're reading this I assume you made it through the whole thing so please let me know what you think! Reviews are always welcome!**


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